Serious Scientific Stuff

My day-job is a Researcher at Wageningen University, the Netherlands.

I got my BSc and MSc in plant breeding, after which I landed this PhD in horticulture.

Here are some works I have published.

Horticultural Plant Journal

Additional far-red light promotes adventitious rooting of double-root-cutting grafted watermelon seedlings

Xue Wu, Xiaoyan Zhang, Yaya Wang, Cuinan Wu, Yudong Sun, Yi Zhang, Yongran Ji, Encai Bao, Liru Xia, Zhonghua Bian, Kai Cao

Root regeneration is an important factor influencing the healing rate of graft union and the survival of double-root-cutting grafting. To date, little information is available on how to enhance root regeneration of rootstock in grafted watermelon (Citrullus lanatus) seedlings. In this study, the effects of different light treatments on root regeneration were determined. This revealed that addition of far-red light (Fr) could significantly expedite root formation in the rootstock. Moreover, the results of transcriptome analysis revealed that plant hormone pathway and auxin-related genes were greatly induced by Fr, especially for auxin-response proteins (including CmIAA11, CmIAA17, and CmAUX28), Small auxin-up RNA genes (including CmSAUR20 and CmSAUR50) and the auxin efflux transporter (CmPIN3). In addition, the expression of Phytochrome Interacting Factor (PIFs), such as CmPIF1, CmPIF3 and CmPIF7, was remarkably increased by Fr. These genes may act together to activate auxin-related pathways under Fr treatment. Based on the results of HPLC-MS/MS analysis, the concentrations of different auxin-types in adventitious root were significantly influenced by Fr. Furthermore, the better growth of rootstock root displayed superior vasculature transport activity of the graft union with Fr treatment, which was determined by the acid magenta dyeing experiment. Therefore, all the results suggested that Fr could induce AR formation in rootstocks, which may be associated with the auxin accumulation by regulating the transcriptional level of auxin-related and PIF genes. The findings of this study demonstrated a practicable way to shorten the healing period of graftings and improve the quality of grafted watermelon seedlings, which will provide a theoretical basis for the speeding development of industrialized seedlings production.

https://doi.org/10.1016/j.hpj.2022.11.012

Journal of Chromatography A

Identification of variety-specific metabolites of basil by high performance thin layer chromatography-assisted metabolic profiling techniques

Windi Putri Wulandari, Yongran Ji, Özlem Erol, Young Hae Choi

The technological advances of analytical instrumentation and techniques has laid the ground for the rapid expansion of metabolomics or in a wider sense, untargeted analysis applied to life sciences themes. However, the objective of identifying all existing metabolites within organisms remains a daunting challenge. All analytical techniques exhibit varying degrees of sensitivity and versatility for the detection of metabolites and none of the existing analytical platforms can be expected to be ideal for exhaustive chemical profiling. Planar liquid chromatography, and in particular, high performance thin layer chromatography (HPTLC), has been used for chemical profiling of natural products in conjunction with metabolomics. HPTLC has specific advantages which include its ability to generate reliable chemical fingerprinting data and facilitate preparative work for metabolite isolation during later stages of metabolomics analysis. In this study, we investigated the chemical profiles of four commercially available basil cultivars, namely Dolly, Emily, Keira, and Rosie. We used HPTLC as the primary analytical tool for the separation of basil cultivars based on detected metabolites, and then compared the results with those obtained with other analytical platforms. We identified the characteristic marker compounds of each basil cultivar from the HPTLC plates and validated their potential using LC-MS and GC-MS analyses as a metabolomics tool. Firstly, we compared the HPTLC data of the four cultivars, obtained with two systems that used silica gel 60 and two mobile phases composed of toluene-EtOAc (8:2, v/v) and EtOAc-formic acid-acetic acid-water (100:11:11:27, v/v), with 1H NMR data to evaluate their separation power. Despite providing lower resolution and detecting fewer compounds, the HPTLC separation power was comparable, and in some cases even better than that of 1H NMR. Additionally, we investigated the potential of HPTLC as a tool for chemical fingerprinting and demonstrated its suitability for preparative purposes that are essential for identifying metabolites in mixture analysis. Metabolites were easily isolated from sample mixtures, and identified with the assistance of GC-MS, LC-MS, and TLC-densitometry.. Several marker compounds were thus identified, including 2,4 di-tertbutylphenol, palmitic acid, hexadecanamide, 9-octadecenamide, squalene, hentriacontane, methyl 3-(3,5-ditert-butyl-4-hydroxyphenyl)propanoic acid, sagerinic acid, and cyanidin-3-O-sophoroside.

https://doi.org/10.1016/j.chroma.2023.464425

Environmental and Experimental Botany:

Phytochrome B1/B2 and auxin transport are involved in the regulation of shoot: root ratio by far-red radiation in tomato

Yongran Ji, Jarno Mooren, Leo F. M. Marcelis, Ep Heuvelink

Plants possess a set of photoreceptors to perceive changes in the light spectrum. Phytochromes (PHY) B1/B2 sense changes in red: far red ratios and are involved in mediating the shade-avoidance responses (SAR) in tomato. Far red (FR) increases the fraction of dry mass partitioning to the shoot at the expense of the root in tomato, but the control of this response has not yet been explained. We studied the role of phytochromes and auxin transport in the regulation of shoot: root ratio. We hypothesized that a loss-of-function mutation in phyB1/B2 leads to a strong increase in shoot: root ratio, similar to the effect of reduced R: FR ratio in wildtype plants. We also hypothesized that the phyB1/B2 double mutation suppresses shoot: root ratio responses when exposed to a reduced R: FR ratio. Furthermore, we hypothesized that the increased shoot: root ratio is linked to the changes in auxin transport between shoot and root. To test these hypotheses, we conducted an experiment in a climate chamber where both wildtype and phyB1/B2 double mutant tomato plants (Solanum lycopersicum cv. Moneymaker) were grown for 21 days with 0, 55 or 85 μmol m−2 s−1 FR in a background of white + red LED light at 150 μmol m−2 s−1. On the 14th day, auxin polar transport inhibitor 1-N-naphthylphthalamic acid (NPA) was applied at the shoot-root junction. PhyB1/B2 mutants showed a higher shoot: root ratio than the wildtype plants. Both wildtype and phyB1/B2 mutants responded to FR with an increase in shoot: root ratio. Blocking auxin transport from shoot to root led to an increase in shoot: root ratio for both genotypes under all light conditions. These results suggest that, similar to other SAR responses like stem elongation, the response of shoot: root ratio to additional FR also involves the regulation by phytochromes, possibly via affecting auxin transport between shoot and root.

https://doi.org/10.1016/j.envexpbot.2023.105471

Current Biology

Vertical Farming

Yongran Ji, Paul Kusuma, Leo F. M. Marcelis

Invited by Current Biology, we wrote a Quick Guide about Vertical farming for the prestigious journal Current Biology. In this piece, the authors answered several key questions about vertical farming:

  • What is vertical farming?

  • How does vertical farming compare to traditional agriculture?

  • Is vertical farming sustainable?

  • What should we grow in vertical farms?

  • What research is needed for the future of vertical farming?

Figure thumbnail gr2

https://doi.org/10.1016/j.cub.2023.02.010

Scientia Horticulturae

Gradually increasing light intensity during the growth period increases dry weight production compared to constant or gradually decreasing light intensity in lettuce

Wenqing Jin, Yongran Ji, Dorthe H. Larsen, Yang Huang, Ep Heuvelink, Leo F.M. Marcelis

Highlights

•Gradually increasing light enhanced plant dry weight due to more light interception.

•Gradually decreasing light enhanced the use efficiency of the intercepted light.

•Gradually changing light intensity did not affect the final fresh weight.

•Gradually increasing light enhanced dry matter content, but had no effect on shelf life.

Abstract

The objective of this research was to investigate the effects of gradually increasing or decreasing photosynthetic photon flux density (PPFD) during cultivation compared to a constant PPFD on biomass production. Lettuce plants (Lactuca sativa L. ‘Expertise’) were grown in climate rooms in which every three days the PPFD was increased by 16 µmol m−2 s−1 (from 140 to 300 µmol m−2 s−1 from day 0 to 30), decreased (from 300 to 140 µmol m−2 s−1), or kept constant (221 µmol m−2 s−1), while the total light integral at the end of the cultivation period (30 d) was the same for all three treatments. Gradually increasing PPFD resulted in a 16 or 13% increase in total plant dry weight compared to treatments with decreasing or constant PPFD, respectively. This increase was explained by a higher light interception mainly because, in this treatment, most of the light was provided at the end of the cultivation period when the leaf area index was high. Consequently, the light use efficiency based on incident PPFD was highest when PPFD gradually increased, even though the light use efficiency based on intercepted PPFD was highest when PPFD gradually decreased during cultivation. Despite the higher shoot dry weight when PPFD gradually increased, shoot fresh weight was not significantly affected by the light treatments. This difference in response between fresh and dry weight resulted from a higher shoot dry matter content when PPFD gradually increased. Our results show that gradually increasing PPFD had a positive effect on dry weight accumulation and increased dry matter content, but did not affect the shelf life. So, although vertical farms enable growers to keep all conditions constant, some dynamic variation of conditions might be needed for optimizing the light use efficiency.

https://doi.org/10.1016/j.scienta.2022.111807

Environmental and Experimental Botany

Potential of ethylene in alleviating cold-induced volatile esters loss of ‘Nanguo’ pears by regulating the lipoxygenase pathway

Miaomiao Yao, Xin Zhou, Yongran Ji, Manli Luo, Yangyang Sun, Qian Zhou, Shujuan Ji

Highlights

  • Ethylene plays an important role in the formation of fruit aroma quality of ‘Nanguo’ pears.

  • Exogenous ethylene treatment relieved the loss of esters in cold-stored ‘Nanguo’ pears.

  • Exogenous ethylene treatment restored the aroma quality by promoting ethylene production and signal transduction.

Abstract

The storage period of ‘Nanguo’ pears (Pyrus ussuriensis Maxim.) can be effectively prolonged under low-temperature conditions. However, long-term refrigeration leads to the deterioration of fruit flavor and aroma through the loss of compounds such as volatile esters, resulting in lower commodity value of the stored fruit. In this study, the loss of ester was noted in fruit under long-term storage, evidenced by the reduced variety of esters, lowered contents of critical esters, and reduced total ester contents. Ethylene production was significantly lower in cold-stored samples than in samples without storage or with short-term storage. Linear regression analysis indicated that the loss of volatile esters induced by cold storage was related to low ethylene production. Exogenous ethylene treatment relieved the loss of esters, increased the types and content of esters, and improved the activities of enzymes involved in ester biosynthesis. Further analysis showed that ethylene production was promoted and that expression levels of key genes involved in ethylene signal transduction, including PuERS1, PuEIN4, PuEIN2, PuEIN3, and PuERF1, were upregulated in ET-treated fruit. Hence, it was concluded that the aroma quality of cold-stored ‘Nanguo’ pears can be improved by ethylene treatment due to the induced enhancement of ethylene biosynthesis and signal transduction.

https://doi.org/10.1016/j.envexpbot.2021.104723

Frontiers in Plant Science

Dissecting the Genotypic Variation of Growth Responses to Far-Red Radiation in Tomato

Yongran Ji, Theoharis Ouzounis, Henk J. Schouten, Richard G. F. Visser, Leo F. M. Marcelis and Ep Heuvelink

The recent development of light-emitting diodes (LEDs) and their application in modern horticulture stimulated studies demonstrating that additional far-red (FR) radiation (700–800 nm) increases plant dry mass. This effect of FR has been explained by improved photosynthesis and/or plant architecture. However, the genotypic variation in this response is largely unknown. Here, we aim to explore and explain the genotypic variation in growth responses to additional FR. We expected the genotypic variation in the responses of plant dry mass to additional FR. Further, we hypothesized that a significant improvement of both net assimilation rate (NAR) and leaf area ratio (LAR) is responsible for a strong dry mass increase under additional FR, while some genotypes respond only marginally or even negatively in NAR or LAR under FR, thus resulting in a weak FR effect on plant dry mass. To test these hypotheses, we grew 33 different tomato genotypes for 21 days with 0, 25, or 100 μmol m–2 s–1 of FR added to a common white + red LED background lighting of 150 μmol m–2 s–1. Genotypes responded similarly with respect to plant height, stem dry mass, and shoot:root ratio; i.e., they all increased with increasing FR. However, the response of total plant dry mass varied among genotypes. We categorized the genotypes into three groups (strongly, moderately, and weakly responding groups) based on their relative response in total plant dry mass to FR. Growth component analysis revealed that the strongly responding genotypes increased strongly in NAR rather than LAR. The weakly responding genotypes, however, showed a substantial increase in LAR but not NAR. The increase in LAR was due to the increase in specific leaf area. Leaf mass fraction, which is the other component of LAR, decreased with FR and did not differ between groups. In conclusion, tomato genotypes that increased strongly in NAR in response to FR were able to achieve a more substantial increase in dry mass than did other genotypes. This is the first study to explain the differences in growth responses of a large number of tomato genotypes toward FR in their light environment.

https://doi.org/10.3389/fpls.2020.614714

New Phytologist

Far‐red radiation stimulates dry mass partitioning to fruits by increasing fruit sink strength in tomato

Yongran Ji, Diego Nuñez Ocaña, Daegeun Choe, Dorthe H. Larsen, Leo F.M. Marcelis, Ep Heuvelink

Summary

•Far‐red (FR) promotes fruit growth by increasing dry mass partitioning to fruits, but the mechanism behind this is unknown. We hypothesise that it is due to an increased fruit sink strength as FR enhances sugar transportation and metabolism.

•Tomato plants were grown with or without 50‐80 μmol m‐2 s‐1 of FR added to a common background 150‐170 μmol m‐2 s‐1 red+blue LED lighting. Potential fruit growth, achieved by pruning each truss to one remaining fruit, was measured to quantify fruit sink strength. Model simulation was conducted to test whether the measured fruit sink strength quantitatively explains the FR effect on dry mass partitioning. Starch, sucrose, fructose, and glucose content were measured. Expression levels of key genes involved in sugar transportation and metabolism were determined.

•FR increased fruit sink strength by 38%, which, in model simulation, led to an increased dry mass partitioned to fruits that quantitatively agreed very well with measured partitioning. FR increased fruit sugar concentration and up‐regulated expression of genes associated with both sugar transportation and metabolism.

•This is the first study to demonstrate that FR stimulates dry mass partitioning to fruits mainly by increasing fruit sink strength via simultaneous up‐regulation of sugar transportation and metabolism.

https://doi.org/10.1111/nph.16805

Environmental & Experimental Botany

Far-red radiation increases dry mass partitioning to fruits but reduces Botrytis cinerea resistance in tomato

Yongran Ji, Theoharis Ouzounis, Sarah Courbier, Elias Kaiser, Phuong T. Nguyen, Henk  J. Schouten, Richard G. F. Visser, Ronald Pierik, Leo F. M. Marcelis, Ep Heuvelink.

Highlights

•Far-red radiation increased tomato fruit production.

•Far-red significantly affected dry mass partitioning pattern in tomato.

•Higher fruit dry mass fraction explained far-red increased fruit production.

•Far-red reduced resistance against Botrytis cinerea in tomato leaves.

Abstract

The addition of far-red (FR, 700–800 nm) radiation to standard growth light triggers a set of photomorphogenic responses collectively termed shade avoidance syndrome. Recent research showed that additional FR increased fruit yield in greenhouse tomato production. However, the mechanism behind this increase is not clear; nor is it known whether there is a trade-off between growth and defense against plant diseases in tomato under additional FR. The aims of this study were 1) to quantify the effect of additional FR on tomato fruit growth, 2) to explain this effect based on underlying growth components and 3) to examine the FR effect on resistance against the necrotrophic fungus Botrytis cinerea. Tomato (Solanum lycopersicum ‘Moneymaker’) plants were grown for four months with 30 or 50 μmol m−2 s−1 of FR added to 150 μmol m−2 s−1 red + blue or white background LED lighting. Growth and development parameters were recorded, and a growth component analysis was conducted. Bioassays for resistance against B. cinerea were conducted on leaf samples collected from each light treatment. Additional FR increased total fruit dry mass per plant by 26–45%. FR affected multiple growth components, among which the fraction of dry mass partitioned to fruits was the most prominent with a 15–35% increase. Truss appearance rate was increased 11–14% by FR while instantaneous net photosynthesis rate was not affected. FR also resulted in more severe disease symptoms upon infection with B. cinerea. In conclusion, additional FR increases tomato fruit production mainly by increasing dry mass partitioning to fruits, rather than improving photosynthesis or increasing total plant biomass. However, FR also reduces resistance of tomato leaves against B. cinerea.

https://doi.org/10.1016/j.envexpbot.2019.103889

Postharvest Biology & Technology

Far-red light during cultivation induces postharvest cold tolerance in tomato fruit

Fahrizal Y. Affandi, Julian C. Verdonk, Theoharis Ouzounis, Yongran Ji, Ernst J.Woltering, Rob E. Schouten

Highlights
•Far-red lighting during cultivation results in firmer red tomatoes at harvest.

•Far-red lighted tomatoes show less weight loss, decay and pitting after cold storage.

•Far-red lighted green tomatoes show faster red colouration after long cold storage.

•Far-red lighted green tomatoes soften less after prior short cold storage.

•In conclusion: Far-red cultivated tomatoes have higher postharvest cold tolerance.

Abstract

We investigated the role of far-red LED light during cultivation on postharvest cold tolerance in tomato fruit (Solanum lycopersicum cv Moneymaker). Red and blue top LED light, providing 150 μmol m−2 s-1 photo-synthetically active radiation (PAR) at plant height for 16 h daily, was combined with 0, 30 or 50 μmol m−2 s-1 (non-PAR) far-red LED light. Tomatoes were harvested at the mature green or red stage and subjected to cold storage for 0, 5, 10, and 15 d at 4 °C, followed by 20 d shelf-life at 20 °C.Mature green harvested tomatoes, cultivated with additional far-red light, showed reduced weight loss, less pitting, faster red colour development during shelf-life (when prior long cold stored), and less softening (when prior short or non-cold stored). FR lighting during cultivation likely protects the membrane integrity of MG tomatoes and thus allows uninterrupted lycopene synthesis. Red harvested tomatoes cultivated with additional far-red light were firmer at harvest, showed reduced weight loss and less decay during shelf-life. Less red colouration was observed for red harvested fruits at the start of shelf-life when fruits were prior cold stored, indicative of lycopene breakdown during cold storage. The improved cold tolerance of red harvested fruits grown under additional far-red light is likely due to higher firmness at the start of the shelf-life period with lycopene acting as antioxidant during cold storage. In conclusion, additional far-red light during cultivation improved postharvest cold tolerance for tomatoes harvested at both the green and red maturity stage, and might therefore be suitable to prolong the storage potential of tomato at sub-optimal temperatures.

Effect of ambient temperature fluctuation on the timing of the transition to the generative stage in cauliflower

Environmental & Experimental Botany

XX Sun, J Bucher, Y Ji, ADJ Van Dijk, RGH Immink, G Bonnema

Cauliflower (Brassica oleracea ssp. botrytis) is an important vegetable that is grown worldwide from the tropics to temperate zones. The harvested product is the curd, which consists of arrested inflorescence meristems. The switch from vegetative development to curd formation in cauliflower, referred to as the generative switch, is strongly temperature responsive in the majority of varieties. We aimed at measuring the delay in timing of the generative switch by high ambient temperature, and how temperature affects the expression of genes with a potential role in timing of this switch. A seven day increase of six degrees in day and night temperature during vegetative development, results in a substantial delay of the generative switch and increased variation in timing of this switch in sensitive cultivars only. The expression level of the Cauliflower FRUITFULL-like gene BoFULcincreased significantly at the generative switch and therefore can be used as marker for this developmental phase change. The expression profiles of the majority of the other investigated cauliflower flowering time genes resembled the expression behaviour of their homologous genes in the model plant Arabidopsis thaliana during the vegetative stage and flowering induction. An exception was the expression of two FLC paralogues BoFLC-1 and BoFLC-3, which showed opposite expression profiles of which the pattern of BoFLC-1 resembles the pattern expected based on Arabidopsis FLC. This interesting observation suggests different roles for these two FLC paralogs in regulation of the timing of the generative switch in cauliflower. Unexpectedly, high temperatures did not delay timing of expression of the majority of investigated genes in meristems and leaves of sensitive cultivars that were delayed in the switch to the generative stage. However, expression of a few potential flowering-time genes was affected by the high temperature treatment in a sensitive cultivar, making them potential candidates to be causal for the observed delay in generative switch.

https://www.sciencedirect.com/science/article/pii/S0098847218301448

Blue and red LED lighting effects on plant biomass, stomatal conductance, and metabolite content in nine tomato genotypes

Acta Horticulturae

T. Ouzounis, E. Heuvelink, Y. Ji, H.J. Schouten, R.G.F. Visser, L.F.M. Marcelis

A collection of nine tomato genotypes was chosen based on their diversity, phylogeny, availability of genome information, and agronomic traits. The objective of the study was to characterize the effect of red and blue LED (light-emitting diode) lighting on physiological, morphological, developmental, and chemical parameters. Two LED light treatments were imposed: (1): 100% red and (2): 88% red/12% blue (peak emission at 662 and 456 nm for red and blue light, respectively). The combination of blue and red LED lighting increased total dry matter in seven of the nine genotypes compared to red. Upward or downward leaf curling was observed in all genotypes in the 100% red treatment. Stomatal conductance was not affected much by additional blue light, but blue light increased chlorophyll and flavonol contents in three genotypes. The exposure of tomato plants to a combination of red and blue LEDs alleviated leaf morphological abnormalities and enhanced plant biomass, and variably affected stomatal conductance and secondary metabolism compared to red light alone.

https://www.actahort.org/books/1134/1134_34.htm

Perspectives for breeding for nitrogen efficiency in head cabbage: Literature review (in Dutch).

A Hospers-Brands, Y Ji, PC Struik, ET Lammerts van Bueren

Cabbage is an important crop in the Netherlands. Brassica species require high levels of nitrogen (ca. 300 kg N/ha) for a good crop growth, often more than can be delivered in an organic rotation within the current regulations for organic agriculture. Nitrogen increases the yield but at high levels of nitrogen the yield reaches a ceiling. In the past much research has been conducted to optimise fertiliser application. To further advance sustainable crop management an important question is which cultivars are robust enough to produce an economically acceptable and stable yield under low nitrogen input levels and under variable weather and growing conditions. It is also relevant to assess which plant traits are associated with nitrogen efficiency. Through literature research, expert consultations and farmer field visits, the perspectives are explored to breed for improved nitrogen efficiency in Brassica types, especially head cabbage. Nitrogen efficiency is the resultant of two component traits: nitrogen uptake efficiency and nitrogen utilisation efficiency. These traits should always be considered in relation to each other as genotypes can combine different strategies to cope with low availability of nitrogen. Most research on nitrogen efficiency in Brassica has been conducted for oil seed rape, Chinese cabbage and cauliflower. However, in our research we found interesting clues to improve nitrogen efficiency in head cabbage. For the uptake capacity a good rooting system is a prerequisite. Apparently, cabbage is able to root until great depth and is capable of capturing nitrogen efficiently from the soil. However, no research is available on genetic variation in rooting characteristics (depth, density, and plasticity) in cabbage under low nitrogen availability. As in organic fertility management nitrogen is less available through mineralisation under cold stress, it is important to include early cultivars in the research. It also became clear from the literature review that in order to properly explore genetic variation in root systems diverse locations should be included as genetic variation is not always expressed at all sites. From the literature we learned that for cabbage most benefits are to be expected from improved nitrogen utilisation efficiency. It appears to be important that the outer leaves remain active until harvest to enhance nitrogen uptake. Also the redistribution from older outer leaves to the young inner leaves forming the head and photosynthetically inactive is relevant. These physiological aspects of utilisation, the ratio between outer and inner leaves (head), and related processes can differ among early, mid-early, and late cultivars. Future research should explore the most ideal ratio between outer leaves and head (harvest index) in relation to nitrogen efficiency, and to what extent leaf attitude and leaf canopy development play a role. In addition it will be interesting to assess whether also other selection criteria can be applied, e.g. leaf area index, specific leaf area index, nitrate reductase activity and / or chlorophyll content or fluorescence.

http://www.louisbolk.org/nl/publicaties/publicatie/?pubID=2896